The evolutionary dynamics of microRNAs in domestic mammals
暂无分享,去创建一个
Wilfried Haerty | Simon Moxon | F. Di Palma | W. Haerty | S. Moxon | L. Penso-Dolfin | Federica Di Palma | Luca Penso-Dolfin | Simon Moxon | Luca Penso-Dolfin
[1] Zhengwei Zhu,et al. CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..
[2] K. Lindblad-Toh,et al. Genome-wide association mapping identifies multiple loci for a canine SLE-related disease complex , 2010, Nature Genetics.
[3] H. Garreau,et al. The genetic structure of domestic rabbits. , 2011, Molecular biology and evolution.
[4] Jeremiah D. Degenhardt,et al. A Simple Genetic Architecture Underlies Morphological Variation in Dogs , 2010, PLoS biology.
[5] Matko Bosnjak,et al. REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms , 2011, PloS one.
[6] Sujatha Kannan,et al. Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny , 2012, BMC Bioinformatics.
[7] A. Quinlan. BEDTools: The Swiss‐Army Tool for Genome Feature Analysis , 2014, Current protocols in bioinformatics.
[8] F. Slack,et al. The evolution of animal microRNA function. , 2007, Current opinion in genetics & development.
[9] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[10] K. Lindblad-Toh,et al. The genomic signature of dog domestication reveals adaptation to a starch-rich diet , 2013, Nature.
[11] Eugene Berezikov,et al. Evolution of microRNA diversity and regulation in animals , 2011, Nature Reviews Genetics.
[12] Ilan Gronau,et al. Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs , 2016, PLoS genetics.
[13] D. A. Magee,et al. Genome-Wide microRNA Binding Site Variation between Extinct Wild Aurochs and Modern Cattle Identifies Candidate microRNA-Regulated Domestication Genes , 2017, Front. Genet..
[14] Hui Jiang,et al. An in vivo genome wide gene expression study of circulating monocytes suggested GBP1, STAT1 and CXCL10 as novel risk genes for the differentiation of peak bone mass. , 2009, Bone.
[15] C. Gieger,et al. Genome Wide Meta-analysis Highlights the Role of Genetic Variation in RARRES2 in the Regulation of Circulating Serum Chemerin , 2014, PLoS genetics.
[16] V. Ambros,et al. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.
[17] S. Cohen,et al. Temporal Reciprocity of miRNAs and Their Targets during the Maternal-to-Zygotic Transition in Drosophila , 2008, Current Biology.
[18] Bronwen L. Aken,et al. Analyses of pig genomes provide insight into porcine demography and evolution , 2012, Nature.
[19] M. Yerle,et al. Investigation of candidate genes for meat quality in dry-cured ham production: the porcine cathepsin B (CTSB) and cystatin B (CSTB) genes. , 2002, Animal genetics.
[20] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[21] Vincent Moulton,et al. The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets , 2012, Bioinform..
[22] Armand Sánchez,et al. A Genetic Predictive Model for Canine Hip Dysplasia: Integration of Genome Wide Association Study (GWAS) and Candidate Gene Approaches , 2015, PloS one.
[23] Chung-I Wu,et al. The evolution of evolvability in microRNA target sites in vertebrates , 2013, Genome research.
[24] Eric C Lai,et al. Mirtrons: microRNA biogenesis via splicing. , 2011, Biochimie.
[25] Jie Wu,et al. deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data , 2015, Nucleic Acids Res..
[26] T. Marquès-Bonet,et al. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs , 2015, Proceedings of the National Academy of Sciences.
[27] C. Bendixen,et al. Advances in porcine genomics and proteomics--a toolbox for developing the pig as a model organism for molecular biomedical research. , 2010, Briefings in functional genomics.
[28] Sebastian D. Mackowiak,et al. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades , 2011, Nucleic acids research.
[29] Göran Andersson,et al. Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development—Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus , 2016, PLoS genetics.
[30] V. Kim,et al. Regulation of microRNA biogenesis , 2014, Nature Reviews Molecular Cell Biology.
[31] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[32] D. Bartel,et al. Predicting effective microRNA target sites in mammalian mRNAs , 2015, eLife.
[33] Leif Andersson,et al. Prehistoric genomes reveal the genetic foundation and cost of horse domestication , 2014, Proceedings of the National Academy of Sciences.
[34] D. Bartel. MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.
[35] K. Worley,et al. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution , 2009, Science.
[36] James A. Cuff,et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog , 2005, Nature.
[37] Janet Kelso,et al. PatMaN: rapid alignment of short sequences to large databases , 2008, Bioinform..
[38] E. Sontheimer,et al. Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.
[39] James J. Cai,et al. Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy , 2016, BMC Genomics.
[40] P. Khaitovich,et al. Birth and expression evolution of mammalian microRNA genes , 2013, Genome research.
[41] K. Lindblad-Toh,et al. Genome-wide association analysis reveals a SOD1 mutation in canine degenerative myelopathy that resembles amyotrophic lateral sclerosis , 2009, Proceedings of the National Academy of Sciences.
[42] Thomas Lengauer,et al. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure , 2006, Bioinform..
[43] I. Hofacker. RNA Secondary Structure Analysis Using the Vienna RNA Package , 2003, Current protocols in bioinformatics.
[44] Ping Xu,et al. miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets , 2017, Bioinform..
[45] Qinghua Shi,et al. mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing , 2013, RNA biology.
[46] Adam Powell,et al. The genetic prehistory of domesticated cattle from their origin to the spread across Europe , 2015, BMC Genetics.
[47] A. Siepel,et al. Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus , 2017, bioRxiv.
[48] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[49] N. Rajewsky,et al. Deep conservation of microRNA-target relationships and 3'UTR motifs in vertebrates, flies, and nematodes. , 2006, Cold Spring Harbor symposia on quantitative biology.
[50] C. Burge,et al. Most mammalian mRNAs are conserved targets of microRNAs. , 2008, Genome research.
[51] Anne Schnoebelen. Mass , 2018, Oxford Bibliographies Online Datasets.
[52] D. Bickhart,et al. Genomic signatures reveal new evidences for selection of important traits in domestic cattle. , 2015, Molecular biology and evolution.
[53] Sam Griffiths-Jones,et al. miRBase: the microRNA sequence database. , 2006, Methods in molecular biology.
[54] E. Wolf,et al. Completion of the swine genome will simplify the production of swine as a large animal biomedical model , 2012, BMC Medical Genomics.
[55] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.
[56] H. Garreau,et al. Levels and Patterns of Genetic Diversity and Population Structure in Domestic Rabbits , 2015, PloS one.
[57] Steven G. Schroeder,et al. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle , 2015, Genome Biology.
[58] K. Schachtschneider,et al. Unraveling the swine genome: implications for human health. , 2015, Annual review of animal biosciences.
[59] Caleb Webber,et al. GAT: a simulation framework for testing the association of genomic intervals , 2013, Bioinform..
[60] D. Larkin,et al. Cattle genomics and its implications for future nutritional strategies for dairy cattle. , 2013, Animal : an international journal of animal bioscience.
[61] Galt P. Barber,et al. BigWig and BigBed: enabling browsing of large distributed datasets , 2010, Bioinform..
[62] Bruce A. Hay,et al. The Drosophila MicroRNA Mir-14 Suppresses Cell Death and Is Required for Normal Fat Metabolism , 2003, Current Biology.
[63] R. Russell,et al. bantam Encodes a Developmentally Regulated microRNA that Controls Cell Proliferation and Regulates the Proapoptotic Gene hid in Drosophila , 2003, Cell.